Project Details
Projekt
Mechanisms of polysaccharide degradation in particle-associated microbial communities
Subject Area
Microbial Ecology and Applied Microbiology
Term
from 2016 to 2024
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 277249973
Microbial processes in marine particles are central to carbon cycling in the oceans, as they determine the fate of phytoplankton-produced carbon. Particle-associated (PA) bacteria degrade complex polysaccharides, thereby preventing them from becoming a carbon sink on the ocean floor. A large fraction of particles are eukaryotic microorganisms such as living or dead phytoplankton. In B3, we tackle the complexity of these particles using metagenomic and metaproteomic techniques on natural phytoplankton blooms in combination with targeted isolation and physiological characterization of PA bacterial strains in culture. We developed a novel metaproteomics pipeline to analyze the particle fraction and applied this to the phytoplankton bloom in 2018, uncovering unique adaptations of the PA lifestyle. With co-occurrence network analyses based on rRNA gene amplicon sequencing, we revealed distinct bacterial communities associated with particles containing either diatoms or dinoflagellates. With subproject B1, we showed that metagenome-assembled genomes of these bacteria reflect specific algal-bacterial interactions. On the basis of long-read metagenome sequencing, we were further able to assemble eukaryotic genomes from particles, which opens up enormous potential for addressing interactions between phytoplankton and bacteria in polysaccharide degradation. The introduction of sedimentation cones further enabled us to identify model bacteria with a particle-associated or -attached lifestyle. Further, we established a collection of PA bacteria. Of these, Muricauda and Maribacter strains were selected as model PA bacteria for the proteomic analysis of cells grown on different polysaccharides. Proteomic analyses identified the expression of novel glycosyl hydrolases with unknown substrate specificity. In Maribacter, natural microalgal cell walls as a substrate induced highly similar proteome patterns as arabinogalactan. In the third phase of subproject B3, we expand the exploration of particle microbiomes and, in particular, of their eukaryotic component by including new PI, an expert in eukaryote genomics. By assembling and annotating eukaryotic genomes from metagenomic data, we will push the current boundaries for interpreting the complexity of marine particles. Coupled with an unprecedented high-resolution metaproteomic analysis of the spring bloom of 2020, as well as more sophisticated bacterial-phytoplankton co-occurrence network analysis, we will be able to shed light on both the eukaryotic and bacterial sides of phytoplankton-bacterial interactions and their impact on degradation as well as synthesis of polysaccharides. Furthermore, we plan to biochemically characterize bacterial enzymes which are induced during transformations of substrates typical of marine particles, expanding our understanding of the diversity of marine polysaccharide-active enzymes.
DFG Programme
Research Units
